AMBER Archive (2005)

Subject: RE: AMBER: error with compiling amber8 with lam on intel pc clusters

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Dec 15 2005 - 10:11:05 CST

Dear Ye,

Try downloading the lam source code and compiling your own version of lam
using the same compilers as you are using to compile amber. From the error
it looks like Lam was built with PGI but AMBER with the Intel compiler. I
highly recommend rebuilding lam with the Intel compiler. Make sure all the
paths are correct, i.e. you LD_LIBRARY_PATH only contains the intel
libraries and not the PGI ones as well. It is also probably best to remove
any PGI directories from your path to avoid potential conflicts over which
libraries are actually used.

All the best
Ross

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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Ye Mei
> Sent: Wednesday, December 14, 2005 19:37
> To: amber mailing list
> Subject: AMBER: error with compiling amber8 with lam on intel
> pc clusters
>
> Dear Amber users，
>
> when I tried to compile amber8 with lam and ifort on my intel
> pc cluster, it failed with error message:
> ifort -FR -o sander trace.o lmod.o decomp.o icosasurf.o
> egb.o findmask.o pb_force.o sander.o cshf.o noecalc.o
> noeread.o caldis.o calrate.o dinten.o drates.o indexn.o
> kmat.o pearsn.o plane.o remarc.o nmrcal.o nmrred.o restal.o
> getnat.o nmrnrg.o modwt.o disnrg.o angnrg.o tornrg.o nmrprt.o
> nmrgrp.o nmrcms.o nmrcmf.o impnum.o nmrsht.o at2res.o
> chklin.o opnmrg.o printe.o runmin.o ndvprt.o force.o rdparm.o
> mdread.o locmem.o runmd.o getcor.o r6ave.o r6drv.o aveint.o
> degcnt.o corf.o threeb.o tripl.o nmrrad.o decnvh.o fastwt.o
> echoin.o parallel.o jnrg.o shake.o ene.o mdwrit.o minrit.o
> set.o setmm.o dynlib.o mdfil.o nmlsrc.o ew_force.o ew_setup.o
> ew_box.o ew_bspline.o ew_fft.o ew_direct.o ew_recip.o
> pcshift.o align.o rstack.o istack.o rfree.o rgroup.o random.o
> lsqfit.o amopen.o debug.o ew_recip_reg.o ew_handle_dips.o
> ew_dipole_recip.o mexit.o new_time.o extra_pts.o thermo_int.o
> matinv.o assert.o mmtsb.o mmtsb_client.o erfcfun.o veclib.o
> mdm.o pb_init.o constantph.o prn_dipoles.o \
> ../lmod/lmod.a -L/usr/local/lam/lib -llammpio
> -llamf77mpi -lmpi -llam -lutil -lpthread -lsvml
> -L/usr/intel/imkl/mkl80/lib/32 -lvml -lmkl_lapack64 -lmkl
> -lguide -lpthread \
> ../lapack/lapack.a ../blas/blas.a ../lib/nxtsec.o ../lib/sys.a
> /usr/local/lam/lib/libmpi.a(lamonesided.o)(.text+0x876): In
> function `lam_accumulate':
> : undefined reference to `__mth_i_kmul'
> /usr/local/lam/lib/libmpi.a(lamonesided.o)(.text+0x972): In
> function `lam_accumulate':
> : undefined reference to `__mth_i_kmul'
> /usr/local/lam/lib/libmpi.a(lamonesided.o)(.text+0xaea): In
> function `lam_put':
> : undefined reference to `__mth_i_kmul'
> /usr/local/lam/lib/libmpi.a(lamonesided.o)(.text+0xb7a): In
> function `lam_get':
> : undefined reference to `__mth_i_kmul'
> /usr/local/lam/lib/libmpi.a(lamreduce.o)(.text+0x341): In
> function `lam_max':
> : undefined reference to `__mth_i_kcmp'
> /usr/local/lam/lib/libmpi.a(lamreduce.o)(.text+0x3b5): In
> function `lam_max':
> : undefined reference to `__mth_i_kucmp'
> /usr/local/lam/lib/libmpi.a(lamreduce.o)(.text+0x761): In
> function `lam_min':
> : undefined reference to `__mth_i_kcmp'
> /usr/local/lam/lib/libmpi.a(lamreduce.o)(.text+0x7d5): In
> function `lam_min':
> : undefined reference to `__mth_i_kucmp'
> /usr/local/lam/lib/libmpi.a(lamreduce.o)(.text+0x1169): In
> function `lam_prod':
> : undefined reference to `__mth_i_kmul'
> /usr/local/lam/lib/libmpi.a(lamreduce.o)(.text+0x11dc): In
> function `lam_prod':
> : undefined reference to `__mth_i_kmul'
> /usr/local/lam/lib/libmpi.a(types.o)(.data+0x2c): In function
> `lam_tv_load_type_defs':
> /root/lam-7.0.4/share/mpi/totalview/types.c:55: undefined
> reference to `__pgdbg_stub'
> make[1]: *** [sander] Error 1
> make[1]: Leaving directory `/home/ymei/amber8/src/sander'
> make: *** [parallel] Error 2
>
> It seems that it need some library of pgi compiler. So I
> tried pgi compiler, and the compilation completed successfully.
> I feel puzzled with this message, especially the last line.
> /root/lam-7.0.4/share/mpi/totalview/types.c:55: undefined
> reference to `__pgdbg_stub'
>
> Who can help me out of it?
> 　　　　　　
>
> Best regards,
>
> Ye Mei
> ymei_at_itcc.nju.edu.cn
> Institute of Theoretical and Computational Chemistry
> Key Laboratory of Mesoscopic Chemistry
> School of Chemistry and Chemical Engineering
> Nanjing University
> Nanjing 210093
> P.R.China
> 2005-12-15
>
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